Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for LYVE1
Basic gene info.Gene symbolLYVE1
Gene namelymphatic vessel endothelial hyaluronan receptor 1
SynonymsCRSBP-1|HAR|LYVE-1|XLKD1
CytomapUCSC genome browser: 11p15
Genomic locationchr11 :10579412-10590365
Type of geneprotein-coding
RefGenesNM_006691.3,
Ensembl idENSG00000133800
Descriptioncell surface retention sequence binding protein-1cell surface retention sequence-binding protein 1extracellular link domain containing 1extracellular link domain-containing 1extracellular link domain-containing protein 1hyaluronic acid receptorlymph
Modification date20141207
dbXrefs MIM : 605702
HGNC : HGNC
HPRD : 05753
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LYVE1
BioGPS: 10894
Gene Expression Atlas: ENSG00000133800
The Human Protein Atlas: ENSG00000133800
PathwayNCI Pathway Interaction Database: LYVE1
KEGG: LYVE1
REACTOME: LYVE1
ConsensusPathDB
Pathway Commons: LYVE1
MetabolismMetaCyc: LYVE1
HUMANCyc: LYVE1
RegulationEnsembl's Regulation: ENSG00000133800
miRBase: chr11 :10,579,412-10,590,365
TargetScan: NM_006691
cisRED: ENSG00000133800
ContextiHOP: LYVE1
cancer metabolism search in PubMed: LYVE1
UCL Cancer Institute: LYVE1
Assigned class in ccmGDBC

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Phenotypic Information for LYVE1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: LYVE1
Familial Cancer Database: LYVE1
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_HYALURONAN_METABOLISM
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: LYVE1
MedGen: LYVE1 (Human Medical Genetics with Condition)
ClinVar: LYVE1
PhenotypeMGI: LYVE1 (International Mouse Phenotyping Consortium)
PhenomicDB: LYVE1

Mutations for LYVE1
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows LYVE1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
There's no copy number variation information in COSMIC data for this gene.

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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=16)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

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check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.
GRCh37 positionMutation(aa)Unique sampleID count
chr11:10585602-10585602p.F94L2
chr11:10580685-10580685p.T314T2
chr11:10585864-10585864p.A48V2
chr11:10585563-10585563p.G107G2
chr11:10582155-10582155p.K197I1
chr11:10582171-10582171p.S192A1
chr11:10585615-10585615p.V90G1
chr11:10580680-10580680p.R316Q1
chr11:10582192-10582192p.P185T1
chr11:10585793-10585793p.D72N1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 31 1 1  32   63 1
# mutation 1 31 1 1  32   63 1
nonsynonymous SNV 1 3  1 1  32   32 1
synonymous SNV    1           31  
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.
Genomic PositionMutation(aa)Unique sampleID count
chr11:10585563p.G107G2
chr11:10582155p.S131L1
chr11:10590003p.L318M1
chr11:10582192p.D72N1
chr11:10580675p.G70D1
chr11:10582227p.R316Q1
chr11:10580680p.L52L1
chr11:10582264p.T314T1
chr11:10580685p.A48V1
chr11:10582327p.T313S1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for LYVE1 in TCGA
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for LYVE1

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))
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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

ABCA6,ABCA8,ABCA9,ANGPTL1,C7,CAV1,CCDC69,
CD209,CHST7,CORO2B,HSPB6,LRRN4CL,LYVE1,MMRN1,
MRAP,NPR1,NR5A2,PTGIS,STAB2,TCF23,TNXB
BCAT1,CD200R1,CD209,CMKLR1,COLEC12,DAB2,F13A1,
FOLR2,FSTL1,GFPT2,GPR1,HPGDS,HRH1,LILRB5,
LYVE1,MFAP5,MPEG1,MRC1,RGL1,SCN9A,SLC24A4

APLNR,CD93,COL15A1,CXorf36,F13A1,GPR116,HTR2A,
IL1R1,LYVE1,NHSL2,NPR1,PREX2,RHOJ,S1PR1,
SHE,STARD8,SV2B,TEK,THBD,THSD7A,TIE1
ABCA6,ABCA9,ADH1B,ALDH1A3,ANXA1,C11orf70,C1S,
C7,CDO1,CYP7B1,FMO2,LOC572558,LOH12CR2,LYVE1,
NRN1,RBP7,RGL1,SETD7,SNCA,SNCG,TPST1
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for LYVE1


There's no related Drug.
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Cross referenced IDs for LYVE1
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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